In my opinion, in general, "we" should fix the mechanics, then adjust the damage numbers. I have a lot of issues with the balance and general game progression tied to items but this would require a simple fix to salvage an important item. Important as in it's part of the game and people should have the option to use it in their melee run progression if they want and not be punished for it.
The major problem with the item is NOT the damage, it's the knockback and how it feels to use the weapon, the whole point of using a sword is to have a wide arc to push enemies away (almost always a useless type of weapon against bosses until you get to the last couple swords). Both the sword and bees should be allowed to hit as soon as contact is made, just lower the sword damage where both the bees and sword deal a significant portion of the damage each so neither mechanic feels useless. Also it should not be balanced with hivepack in mind, it should be an excellent (read very strong) weapon with the hivepack, otherwise you run into the problem where you are forced to use an accessory slot just for that weapon to feel good to use instead of making it feel good to use the hivepack.
So, finally, sword is not a very versatile weapon type (which it shouldn't because then what would be the point of flails, yoyos, spears...), already optimal to use against very few enemies. To give at least one example to what it is good against: a swarm of small bees for example, or against a mobile enemy (read flying hornets, for example) you have trouble hitting with other weapons (you might take damage but the wide arc makes it more reliable damage). Some people might disagree as to what enemies sword are best again but I felt compelled to give examples to make my point. Which is: why this weapon or swords in general gotta be so bad when their usage is already limited. They should be good at what they should be good at, not just meh at it. And currently, beekeeper fails completely at being even an average sword because of that knockback issue. It doesn't keep you safe, it doesn't deal great damage either.